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Boron nitride nanotubes (BNNTs) exhibit a range of properties that hold great potential for many fields of science and technology; however, they have inherently low chemical reactivity, making functionalization for specific applications difficult. Here we propose that covalent functionalization of BNNTs via reduction chemistry could be a highly promising and viable strategy. Through density functional theory calculations of the electron affinity of BNNTs and their binding energies with various radicals, we reveal that their chemical reactivity can be significantly enhanced via reducing the nanotubes (i.e., negatively charging). For example, a 5.5-fold enhancement in reactivity of reduced BNNTs toward NH2 radicals was predicted relative to their neutral counterparts. The localization characteristics of the BNNT π electron system lead the excess electrons to fill the empty p orbitals of boron sites, which promote covalent bond formation with an unpaired electron from a radical molecule. In support of our theoretical findings, we also experimentally investigated the covalent alkylation of BNNTs via reduction chemistry using 1-bromohexane. The thermogravimetric measurements showed a considerable weight loss (12-14%) only for samples alkylated using reduced BNNTs, suggesting their significantly improved reactivity over neutral BNNTs. This finding will provide an insight in developing an effective route to chemical functionalization of BNNTs.

We used a newer, synchrotron-based, spectroscopic technique (nuclear resonance vibrational spectroscopy, NRVS) in combination with a more traditional one (infrared absorption, IR) to obtain a complete, quantitative picture of the metal center vibrational dynamics in a six-coordinated tin porphyrin. From the NRVS (119)Sn site-selectivity and the sensitivity of the IR signal to (112)Sn/(119)Sn isotope substitution, we identified the frequency of the antisymmetric stretching of the axial bonds (290 cm(-1)) and all the other vibrations involving Sn. Experimentally authenticated density functional theory (DFT) calculations aid the data interpretation by providing detailed normal mode descriptions for each observed vibration. These results may represent a starting point toward the characterization of the local vibrational dynamics of the metallic site in tin porphyrins and compounds with related structures. The quantitative complementariness between IR, NRVS, and DFT is emphasized.

Nuclear resonance vibrational spectra have been obtained for six five-coordinate imidazole-ligated iron(II) porphyrinates, [Fe(Por)(L)] (Por = tetraphenylporphyrinate, octaethylporphyrinate, tetratolylporphyrinate, or protoporphyrinate IX and L = 2-methylimidazole or 1,2-dimethylimidazole). Measurements have been made on both powder and oriented crystal samples. The spectra are dominated by strong signals around 200-300 cm(-1). Although the in-plane and out-of-plane vibrations are seriously overlapped, oriented crystal spectra allow their deconvolution. Thus, oriented crystal experimental data, along with density functional theory (DFT) calculations, enable the assignment of key vibrations in the spectra. Molecular dynamics are also discussed. The nature of the Fe-N(Im) vibrations has been elaborated further than was possible from resonance Raman studies. Our study suggests that the Fe motions are coupled with the porphyrin core and peripheral groups motions. Both peripheral groups and their conformations have significant influence on the vibrational spectra (position and shape).

TDDFT calculations, picosecond transient absorption, and time-resolved fluorescence studies of 4-dimethylamino-2-hydroxy-benzaldehyde (DMAHBA) have been carried out to study the electron and proton transfer processes in polar (acetonitrile) and nonpolar (n-hexane) solvents. In n-hexane, the transient absorption (TA) as well as the fluorescence originate from the ππ* state of the keto form (with the carbonyl group in the benzaldehyde ring), which is produced by an intramolecular proton transfer from the initially excited ππ* state of the enol form (OH group in the ring). The decay rate of TA and fluorescence are essentially identical in n-hexane. In acetonitrile, on the other hand, the TA exhibits features that can be assigned to the highly polar twisted intramolecular charge transfer (TICT) states of enol forms, as evidenced by the similarity of the absorption to the TICT-state absorption spectra of the closely related 4-dimethylaminobenzaldehyde (DMABA). As expected, the decay rate of the TICT-state of DMAHBA is different from the fluorescence lifetime of the ππ* state of the keto form. The occurrence of the proton and electron transfers in acetonitrile is in good agreement with the predictions of the TDDFT calculations. The very short-lived (∼1 ps) fluorescence from the ππ* state of the enol form has been observed at about 380 nm in n-hexane and at about 400 nm in acetonitrile.

The photophysics of a prototypical cross-conjugated π-system, 1,1'-diphenylethylene, have been studied using high-resolution resonance enhanced multiphoton ionization excitation spectroscopy and zero kinetic energy photoelectron spectroscopy, in combination with advanced ab initio calculations. We find that the excitation spectrum of S(1) displays extensive vibrational progressions that we identify to arise from large changes in the torsional angles of the phenyl rings upon electronic excitation. The extensive activity of the antisymmetric inter-ring torsional vibration provides conclusive evidence for a loss of symmetry upon excitation, leading to an inequivalence of the two phenyl rings. Nonresonant zero kinetic energy photoelectron spectroscopy from the ground state of the neutral molecule to the ground state of the radical cation, on the other hand, demonstrates that upon ionization symmetry is retained, and that the geometry changes are considerably smaller. Apart from elucidating how removal of an electron affects the structure of the molecule, these measurements provide an accurate value for the adiabatic ionization energy (65274 ± 1 cm(-1) (8.093 eV)). Zero kinetic energy photoelectron spectra obtained after excitation of vibronic levels in S(1) confirm these conclusions and provide us with an extensive atlas of ionic vibronic energy levels. For higher excitation energies the excitation spectrum of S(1) becomes quite congested and shows unexpected large intensities. Ab initio calculations strongly suggest that this is caused by a conical intersection between S(1) and S(2)., (© 2011 American Chemical Society)

We report the results of quantum-chemical calculations, which show that the keto form of 2-hydroxynaphtylidene-(8-aminoquinoline) (HNAQ) is slightly more stable than the enol form both in the ground and first excited ππ* electronic states. The barrier for proton transfer between the enol and the ketone in the ground state is ca. 3300 cm(-1) (HF), and 770 cm(-1) (B3LYP), indicating a very fast (ps scale) exchange of protons between the two tautomeric forms. This barrier decreases slightly in the first excited ππ* electronic state (2500 cm(-1) - CIS), making proton exchange even faster. We show that the ππ* state of the ketone tautomer is prone to radiationless transition to a state with nearly perpendicular orientation of the two ring systems, similarly to other Schiff bases that are photochromes (for instance salicydeneaniline). This state arises when an electron from the highest occupied molecular orbital (HOMO) of the ketone ring system is transferred to a LUMO localized on the CHNH group of the bridge connecting the two ring systems of the molecule. The energy minimum of this "perpendicular" state lies only ca. 0.09 eV from the ground state potential-energy surface, thus it is prone to extremely rapid radiationless decay. Further relaxation on this surface leads to a metastable conformation that lies ca. 4440 cm(-1) above the planar, hydrogen-bonded, ketone conformation. Unfortunately, photochromism of this metastable conformation does not occur, since its absorption spectrum overlaps the spectrum of the stable species (with the predicted absorption around 438 nm vs calculated 440.6 nm in the stable ketone)., (© 2011 American Chemical Society)

The solvent-polarity dependence and temporal characteristics of the transient absorption of 4-(dimethylamino)benzonitrile, DMABN, and 4-(dimethylamino)benzethyne, DMABE, demonstrate the presence of the πσ*-state absorption at about 700 nm and the ππ* (LE)-state absorption at about 520 nm and 450 nm. The rise and decay times of the πσ*-state transient differ from those of the ππ*-state transients in both compounds. Moreover, the peak position of the πσ*-state absorption is blue-shifted and more intense in acetonitrile as compared to n-hexane, whereas the band positions of the ππ*-state absorptions are essentially the same in the two solvents. For DMABN in acetonitrile, the rise time (∼4.3 ps) of the twisted intramolecular charge transfer (TICT)-state transient at 330 nm is identical to the decay time of the πσ*-state transient. The 4.8 ns decay time of the TICT-state absorption of DMABN is longer than the 2.9 ns decay time of the intramolecular charge-transfer (ICT) fluorescence, indicating that the fluorescent ICT state differs from the TICT state observed in transient absorption. These results are consistent with the presence of a low-lying πσ* state in DMABN (and DMABE), and the role the πσ* state plays in the formation of the TICT state of DMABN.

A concerted experi-mental (time-resolved spectroscopies) and computational (TDDFT) study of p-N,N-dimethylamino-p'-cyano-diphenylacetylene (DACN-DPA) has been carried out to probe the intramolecular charge transfer (ICT) reaction that occurs in polar solvents. The picosecond transient absorption, as well as fluorescence, in acetonitrile reveals the formation of a twisted ICT(σ*) state, which involves transfer of an electron from the 4-(dimethylamino)benzethyne moiety (DMAB) to the benzonitrile (BN) group. This ICT(σ*) state, with a large dipole moment (24.7 D) and a geometry in which the plane of electron-accepting BN group is perpendicular to the plane electron-donating DMAB moiety and the angles of C(DMAB)C≡C is 135.0°, is responsible for the greatly Stokes-shifted (∼8000 cm(-1)) fluorescence and the transient absorption bands (with peaks at about 630 and 425 nm), which decays with the same lifetime (∼780 ps). It is proposed that the 630 nm picosecond transient absorption of the ICT state represents the absorption spectrum of dimethylaminobenzethyne radical cation and the 425 nm transient represents the absorption spectrum of benzonitrile radical anion. In nonpolar n-hexane, most of the fluorescence as well as the major component of the transient absorption originate from the S(1) (ππ*) state.

Photosynthesis, which depends on light-driven energy and electron transfer in assemblies of porphyrins, chlorophylls, and carotenoids, is just one example of the many complex natural systems of photobiology. A fuller understanding of the spectroscopy and photophysics of simple aromatic molecules is central to elucidating photochemical processes in the more sophisticated assemblies of photobiology. Moreover, developing a better grasp of the photophysics of simple aromatic molecules will also enhance our ability to create and improve practical applications in photochemical energy conversion, molecular nanophotonics, and molecular electronics. In this Account, we present a concerted experimental and theoretical study of aromatic ethynes, aromatic nitriles, and fluorinated benzenes, illustrating the important roles that the low-lying pisigma* state plays in the electronic relaxation of these aromatic compounds. Diphenylacetylene, 4-dialkylaminobenzonitriles, 4-dialkylaminobenzethynes, and fluorinated benzenes exhibit fluorescence that strongly quenches as the excitation energy is increased for gas-phase systems and at elevated temperatures in solution. Much of this interesting photophysical behavior can be attributed to the presence of a dark intermediate state that crosses the fluorescent pipi* state. Our quantum chemistry calculations, as well as time-resolved laser spectroscopies, indicate that this dark intermediate state is the pisigma* state that arises from the promotion of an electron from the pi orbital of the phenyl ring to the sigma* orbital localized in the C[triple bond]X group (where X is CH and N) or on the C-X group (where X is a halogen). These crossings not only lead to the strong excitation energy and temperature dependence of fluorescence but also induce highly interesting pisigma*-mediated intramolecular charge transfer in 4-dialkylaminobenzonitriles. Most previous studies on the excited-state dynamics of organic molecules have examined aromatic hydrocarbons, nitrogen heterocycles, aromatic carbonyl compounds, and polyenes, which have low-lying excited states of pipi* character (hydrocarbons and polyenes) or npi* and pipi* character (carbonyls and N-heterocycles). These studies have revealed important involvement of selection rules (promoting vibrational modes and spin-orbit coupling) and Franck-Condon factors for radiationless transitions, which have important effects on photophysical properties. The recent experimental and time-dependent density functional theory (TDDFT) calculations of aromatic ethynes, nitriles, and perfluorinated benzenes described in this Account demonstrate the importance of the bound excited state of a pisigma* configuration in these molecules.

A concerted experimental and computational study of 4-(dimethylamino)benzethyne, DMABE, has been carried out to probe the low-lying pisigma* state and the role it plays in the photophysics of the molecule. The subpicosecond transient absorption spectra reveal the presence of a strong excited-state absorption at about 700 nm and a weaker absorption at about 520 nm. The observed absorption maxima are in excellent agreement with the TDDFT calculations that place a strongly allowed pisigma* <--pisigma* transition at 750 nm, and a weaker pipi* <--pipi* (LE) transition at 528 nm. This agreement combined with the differing decay times, and differing solvent shifts of the two transients, allow assignments of the 700 nm absorption to the pisigma* state and the 520 nm absorption to the LE (pipi*) state. The bifurcation of the initially excited L(a) (pipi*) state into the pisigma* state and the LE state, as probed by transient absorption, is strongly influenced by solvent polarity, with polar environments favoring the L(a)-->pisigma* decay channel over the competing L(a)--> LE decay channel. The nanosecond radiationless decay of the LE state to the dark pisigma* state is also strongly enhanced in polar environments, thus accounting for the dramatic quenching of fluorescence in solvents of high polarity.

Time-dependent density functional theory (TDDFT) has been applied to the analysis of the electronic spectra of methylcobalamin (MeCbl) and its derivative in which the trans axial base was replaced by a water molecule (MeCbi[Single Bond]H(2)O). The latter corresponds to the situation encountered in strongly acidic solutions. The study primarily focuses on the accuracy of two functionals, the hybrid B3LYP and the gradient corrected BP86, in dealing with the electronic excitations. The high resolution crystal structure of MeCbl was the source of the initial coordinates. To generate the initial structures, the full MeCbl was simplified by replacing the corrin side chains by H atoms. The vertical excitation energies, together with the corresponding oscillator strengths, were calculated at the optimized BP86 and B3LYP structures of the ground electronic state of the complexes. The NBO analysis shows that the B3LYP functional gives a bonding description of the ground state as a more polarized covalent bond compared to that given by BP86. The latter functional has more covalent bonding and is thus more appropriate for modeling the axial bonding properties. To validate the accuracy of the present TDDFT analysis, the computed excitations were directly compared to the absorption spectra of MeCbl. In order to obtain a reliable agreement between experiment and theory, the two-parameter scaling technique was introduced, which compensates differently the low-energy and high-energy excitations. Electronic excitations strongly depend on the choice of the functional. Transitions involving corrin pi-->pi(*) excitations are better described by the B3LYP functional while transitions associated with metal-to-ligand (dpi-->pi(*)d) excitations are better described by BP86. These differences can be associated with the different bonding descriptions obtained by B3LYP and BP86.

A combination of supersonic-jet laser spectroscopy and quantum chemistry calculation was applied to 1,4-bis(phenylethynyl)benzene, BPEB, to study the role of the dark pisigma* state on electronic relaxation and the effect of ring torsion on electronic spectra. The result provides evidence for fluorescence break-off in supersonic jet at high S1(pi pi*) <-- S0 excitation energies, which can be attributed to the pi pi*-pi sigma* intersection. The threshold energy for the fluorescence break-off is much larger in BPEB (approximately 4000 cm(-1)) than in diphenylacetylene (approximately 500 cm(-1)). The high-energy barrier in BPEB accounts for the very large fluorescence quantum yield of the compound (in solution) relative to diphenylacetylene. The comparison between the experimentally derived torsional barrier and frequency with those from the computation shows overall good agreement and demonstrates that the low-energy torsional motion involves the twisting of the end ring in BPEB. The torsional barrier is almost an order of magnitude greater in the pi pi* excited state than in the ground state. The finding that the twisting of the end ring in BPEB is relatively free in the ground state, but strongly hindered in the excited state, provides rationale for the well-known temperature dependence of the spectral shape of absorption and the lack of mirror symmetry relationship between the absorption and fluorescence at elevated temperatures.

Electronic absorption spectra of the low-lying pipi(*) and pisigma(*) states of several aminobenzonitriles and 4-dimethylaminobenzethyne have been studied by time-resolved transient absorption and time-dependent density functional theory calculation. In acetonitrile, the lifetime of the pisigma(*)-state absorption is very short (picoseconds or subpicosecond) for molecules that exhibit intramolecular charge transfer (ICT), and very long (nanoseconds) for those that do not. Where direct comparison of the temporal characteristics of the pisigma(*)-state and the ICT-state transients could be made, the formation rate of the ICT state is identical to the decay rate of the pisigma(*) state within the experimental uncertainty. These results are consistent with the pisigma(*)-mediated ICT mechanism, L(a) (pipi(*))-->pisigma(*)-->ICT, in which the decay rate of the pisigma(*) state is determined by the rate of the solvent-controlled pisigma(*)-->ICT charge-shift reaction. The pipi(*)-->pisigma(*) state crossing does not occur in 3-dimethylaminobenzonitrile or 2-dimethylaminobenzonitrile, as predicted by the calculation, and 4-aminobenzonitrile and 4-dimethylaminobenzethyne does not exhibit the ICT reaction, consistent with the higher energy of the ICT state relative to the pisigma(*) state.

The substituent at O-2 of glycopyranosides is known to have a pronounced effect on both the formation and the cleavage of glycosides at C-1. This is primarily attributed to stereoelectronic effects on the formation and stability of the related glycopyranosyl oxacarbenium ions. Previous QM studies of 2-O-methyl substituted manno and gluco configured pyranosyl oxacarbenium ions found a preference for the methyl carbon to be syn to the CH-2 methine. This study examines the conformational preference of variously substituted O-2 tetrahydropyranosyl oxacarbenium ions and confirms this syn preference. Neutral analogues are shown to have the expected 3-fold rotation whereas the charged species exhibit 2-fold rotation about C-2-O-2. Natural bond order (NBO) calculations suggest that the dominant stabilizing interaction is a unimodal O-2 lone pair to C-1-O-5 pi-bond hyperconjugative interaction. This syn conformational preference has important implications for mimics of glycopyranosyl oxacarbenium ion transition states. It also suggests a conformational based mechanism that can be exploited to tune the reactivity of glycopyranosyl donors in the glycosylation reaction.

Femtosecond time-resolved photoelectron spectroscopy and high-level theoretical calculations were used to study the effects of methyl substitution on the electronic dynamics of the alpha,beta-enones acrolein (2-propenal), crotonaldehyde (2-butenal), methylvinylketone (3-buten-2-one), and methacrolein (2-methyl-2-propenal) following excitation to the S2(pipi*) state at 209 and 200 nm. We determine that following excitation the molecules move rapidly away from the Franck-Condon region, reaching a conical intersection promoting relaxation to the S1(npi*) state. Once on the S1 surface, the trajectories access another conical intersection, leading them to the ground state. Only small variations between molecules are seen in their S2 decay times. However, the position of methyl group substitution greatly affects the relaxation rate from the S1 surface and the branching ratios to the products. Ab initio calculations used to compare the geometries, energies, and topographies of the S1/S0 conical intersections of the molecules are not able to satisfactorily explain the variations in relaxation behavior. We propose that the S1 lifetime differences are caused by specific dynamical factors that affect the efficiency of passage through the S1/S0 conical intersection.

5,6-Trimethylenecytosine (TMC) and 5,6-trimethyleneuracil (TMU), in which the twist of the C5-C6 bond (or the pyrimidalization of C5) is strongly hindered, do not exhibit the subpicosecond excited-state lifetime characteristic of the naturally occurring pyrimidine bases. This result demonstrates the important role the out-of-plane deformation of the six-membered ring plays in the ultrafast (subpicosecond) internal conversion of photoexcited nucleobases. The dramatically shorter fluorescence lifetime of TMU ( approximately 30 ps) relative to TMC ( approximately 1.2 ns), in aqueous solution at room temperature, is attributed to the presence in TMU of an efficient, secondary nonradiative decay channel of S(1)(pipi*) involving a low-lying (1)npi* state.

We use nuclear resonance vibrational spectroscopy and computational predictions based on density functional theory (DFT) to explore the vibrational dynamics of (57)Fe in porphyrins that mimic the active sites of histidine-ligated heme proteins complexed with carbon monoxide. Nuclear resonance vibrational spectroscopy yields the complete vibrational spectrum of a Mössbauer isotope, and provides a valuable probe that is not only selective for protein active sites but quantifies the mean-squared amplitude and direction of the motion of the probe nucleus, in addition to vibrational frequencies. Quantitative comparison of the experimental results with DFT calculations provides a detailed, rigorous test of the vibrational predictions, which in turn provide a reliable description of the observed vibrational features. In addition to the well-studied stretching vibration of the Fe-CO bond, vibrations involving the Fe-imidazole bond, and the Fe-N(pyr) bonds to the pyrrole nitrogens of the porphyrin contribute prominently to the observed experimental signal. All of these frequencies show structural sensitivity to the corresponding bond lengths, but previous studies have failed to identify the latter vibrations, presumably because the coupling to the electronic excitation is too small in resonance Raman measurements. We also observe the FeCO bending vibrations, which are not Raman active for these unhindered model compounds. The observed Fe amplitude is strongly inconsistent with three-body oscillator descriptions of the FeCO fragment, but agrees quantitatively with DFT predictions. Over the past decade, quantum chemical calculations have suggested revised estimates of the importance of steric distortion of the bound CO in preventing poisoning of heme proteins by carbon monoxide. Quantitative agreement with the predicted frequency, amplitude, and direction of Fe motion for the FeCO bending vibrations provides direct experimental support for the quantum chemical description of the energetics of the FeCO unit.

We present a constrained ab initio molecular dynamics method that allows the modeling of the conformational interconversions of glycopyranosyl oxacarbenium ions. The model was successfully tested by estimating the barriers to ring inversion for two 4-substituted tetrahydropyranosyl oxacarbenium ions. The model was further extended to predict the pathways that connect the (4)H(3) half-chair conformation of 2,3,4,6-tetra-O-methyl-d-glucopyranosyl cation to its inverted (5)S(1) conformation and the (4)H(3) half-chair conformation of 2,3,4,6-tetra-O-methyl-d-mannopyranosyl cation to its inverted (3)E conformation. The modeled interconversion pathways reconcile a large body of experimental work on the acid-catalyzed hydrolysis of glycosides and the mechanisms of a number of glucosidases and mannosidases.

Computational modeling of the enzymatic activity of B12-dependent enzymes requires a detailed understanding of the factors that influence the strength of the Co--C bond and the limits associated with a particular level of theory. To address this issue, a systematic analysis of the electronic and structural properties of coenzyme B12 models has been performed to establish the performance of three different functionals including B3LYP, BP86, and revPBE. In particular the cobalt-carbon bond dissociation energies, axial bond lengths, and selected stretching frequencies have been analyzed in detail. Current analysis shows that widely used B3LYP functional significantly underestimates the strength of the Co--C bond while the nonhybrid BP86 functional produces very consistent results in comparison to experimental data. To explain such different performance of these functionals molecular orbital analysis associated with axial bonds has been performed to show differences in axial bonding provided by hybrid and nonhybrid functionals.

We analyze the electronic and molecular structures for the ground and excited electronic states of aromatic terthiophene (3T), the quinodimethane 3',4'-dibutyl-5,5' '-bis(dicyanomethylene)-5,5' '-dihydro-2,2':5',2' '-terthiophene (3Q), and isologues with the middle ring S-oxidized (3TO2, 3QO2). These represent extremes of electron rich and deficient ground states, often exhibiting complementary properties. Oxidizing the central sulfur atom affects the molecular structure, electron affinity, and photophysical properties of both pi systems. The consequences for 3T include de-aromatization of the central thiophene, red-shifting of the electronic absorption spectrum, and lowering of the reduction potential. The electron deficient quinoid 3QO2 shows an enhancement of electron affinity from reducing the electron-donor ability of sulfur, and a blue-shifting of its electronic absorption spectrum was seen. Fluorescence emission is quenched in the sulfonated terthiophene, and the contrary effect again would be expected upon sulfonation of a quinoid emitter. Raman vibrational spectroscopy, electrochemistry, and UV-vis and fluorescence spectroscopies are analyzed in conjunction with theoretical calculations.

This paper reports on a combined spectroscopic and density functional theory study on a series of cyclo(diacetylenes-oligothiophenes) with different shapes and dimensions. The case of a macrocycle fragmented by the insertion of Pt metallic atoms is illustrated as well. The analysis covers the neutral and oxidized samples. A full assignment of the spectra has been proposed, supported by BP86/cc-pVDZ theoretical calculations. Ring shape and molecular dimension have been related with the C[Double Bond]CC-C structural parameters and Raman wave numbers. Platinum atom insertion within the acetylene spacer seems to soften ring strain owing to the rupture of the strained circular shape. Oxidation causes an overall downshift of the Raman wave numbers likely due to the skeletal relaxation of CC conjugated path, while the ring shape of each macrocycle is conserved upon oxidation.

Density functional theory (DFT)-based normal mode calculations have been carried out on models for B12-cofactors to assign reported isotope-edited resonance Raman spectra, which isolate vibrations of the organo-Co group. Interpretation is straightforward for alkyl-Co derivatives, which display prominent Co-C stretching vibrational bands. DFT correctly reproduces Co-C distances and frequencies for the methyl and ethyl derivatives. However, spectra are complex for adenosyl derivatives, due to mixing of Co-C stretching with a ribose deformation coordinate and to activation of modes involving Co-C-C bending and Co-adenosyl torsion. Despite this complexity, the computed spectra provide a satisfactory re-assignment of the experimental data. Reported trends in adenosyl-cobalamin spectra upon binding to the methylmalonyl CoA mutase enzyme, as well as on subsequent binding of substrates and inhibitors, provide support for an activation mechanism involving substrate-induced deformation of the adenosyl ligand.

The UV chromophores in DNA are the nucleic bases themselves, and it is their photophysics and photochemistry that govern the intrinsic photostability of DNA. Because stability is related to the conversion of dangerous electronic to less-dangerous vibrational energy, we study ultrafast electronic relaxation processes in the DNA base adenine. We excite adenine, isolated in a molecular beam, to its pipi* state and follow its relaxation dynamics using femtosecond time-resolved photoelectron spectroscopy. To discern which processes are important on which timescales, we compare adenine with 9-methyl adenine. Methylation blocks the site of the much-discussed pisigma* state that had been thought, until now, minor. Time-resolved photoelectron spectroscopy reveals that, although adenine and 9-methyl adenine show almost identical timescales for the processes involved, the decay pathways are quite different. Importantly, we confirm that in adenine at 267-nm excitation, the pisigma* state plays a major role. We discuss these results in the context of recent experimental and theoretical studies on adenine, proposing a model that accounts for all known results, and consider the relationship between these studies and electron-induced damage in DNA.

A concerted experimental (mass-selective, double-resonance laser spectroscopic technique) and theoretical (correlated quantum chemistry calculation) study of hydrogen-bonded clusters of 1-cyanonaphthalene (CNN) with water has been carried out to probe geometrical structures of the conformational isomers. The structures of the two low-energy conformers of CNN-H2O and CNN-(H2O)2, calculated at the MP2/cc-pVDZ level of theory, are consistent with the mass-selective infrared-ultraviolet double-resonance spectra and the partially resolved rotational band contours of the S1 <-- S0 origin bands. The facile loss of a neutral water molecule from the cluster ion of CNN-(H2O)2, relative to that of CNN-H2O, is in accord with the proposed structures of the clusters.

Mass-selected resonant two-photon ionization and infrared-ultraviolet double-resonance spectroscopies are combined with correlated (second Moller-Plesset perturbation) quantum chemistry calculation to probe electronic spectra and ground-state geometries of the jet-cooled dimer and higher clusters of 1-cyanonaphthalene. The results indicate that the dimer and trimer have stacked geometries, consistent with the highly efficient, rapid excimer formation that follows photoexcitation of the ground-state clusters.

A series of alpha,omega-bis(mesitylthio)oligothiophenes of various chain lengths and with different side substitution patterns have been studied in their oxidized states by means of electron absorption and Raman spectroscopies in combination with theory in the framework of the density functional theory. Upon chemical oxidation, stable radical cations, dications, and even radical trications are generated. Longer chain lengths better stabilize higher oxidation states. The tetramer can be easily converted to the dication, and a trication can be obtained for the ethylenedioxy derivative. The alpha,omega-sulfur atoms are actively involved in the formation of the charged species and exert a favorable tuning of their electronic structure. Raman spectra provide experimental evidence of the attainment of quinoidal structures within the conjugated path, initially heteroaromatic, with different extension as a function of the p-doping level.

High-resolution X-ray measurements near a nuclear resonance reveal the complete vibrational spectrum of the probe nucleus. Because of this, nuclear resonance vibrational spectroscopy (NRVS) is a uniquely quantitative probe of the vibrational dynamics of reactive iron sites in proteins and other complex molecules. Our measurements of vibrational fundamentals have revealed both frequencies and amplitudes of (57)Fe vibrations in proteins and model compounds. Information on the direction of Fe motion has also been obtained from measurements on oriented single crystals, and provides an essential test of normal mode predictions. Here, we report the observation of weaker two-quantum vibrational excitations (overtones and combinations) for compounds that mimic the active site of heme proteins. The predicted intensities depend strongly on the direction of Fe motion. We compare the observed features with predictions based on the observed fundamentals, using information on the direction of Fe motion obtained either from DFT predictions or from single crystal measurements. Two-quantum excitations may become a useful tool to identify the directions of the Fe oscillations when single crystals are not available.

The conformation of the six-membered ring of pyranosyl sugars has pronounced effects on the physical and chemical properties of carbohydrates. We present a method to determine key features of the potential energy surfaces, such as transition states associated with the inversion pathways of the model compounds cyclohexane, tetrahydropyran, p-dioxane, m-dioxane, s-trioxane, and 2-oxanol. Finally, we make the first determination of the pathways for inversion of penta-O-methyl-alpha-D-glucopyranose and penta-O-methyl-beta-D-glucopyranose. For both anomers, a transition state with five coplanar atoms with appreciable (O)E character was found. The method is based on constrained Car-Parrinello ab initio molecular dynamics, as implemented in the projector augmented-wave (PAW) method. The constraints are derived from the normal modes of six-membered rings and are described in terms of the canonical conformations (1)C(4) chair, (1,4)B boat, and (O)S(2) skew-boat. The PAW derived trajectories are in agreement with previous suggestions in the literature that pseudorotation is an important feature of such conformational interconversions. The dynamic nature as well as the internal coordinate-based constraints provide a method which can reliably accommodate pseudorotation. To determine semiquantitative energies, we recalculate key conformations using standard quantum mechanical calculations while keeping the ring dihedral angles frozen at their values found in the dynamics. In all cases where experimental barriers are known, our results are in excellent agreement.

A theoretical model for the ultrafast S1-->S0 internal conversion of cytosine is presented, in which a state switch from the initially prepared 1pipi* state to the out-of-plane deformed excited state of biradical character controls the rate of the S1(1pipi*) decay. This mechanism successfully accounts for the dramatically longer S1 lifetimes of 5-fluorocytosine and N-acetylcytosine relative to cytosine. The replacement of the C5 hydrogen atom by a methyl group is predicted to lead to a substantial, but not dramatic, increase in the S1 lifetime, also consistent with experiment. It is this ability to correctly predict the substituent effects that distinguishes the present model from the previously proposed mechanisms.

Excitation-energy dependence of fluorescence intensity and fluorescence lifetime has been measured for 4-dimethylaminobenzonitrile (DMABN), 4-aminobenzonitrile (ABN), 4-diisopropylaminobenzonitrile (DIABN), and 1-naphthonitrile (NN) in a supersonic free jet. In all cases, the fluorescence yield decreases rather dramatically, whereas the fluorescence lifetime decreases only moderately for S1 (pi pi*, L(b)) excess vibrational energy exceeding about 1000 cm(-1). This is confirmed by comparison of the normalized fluorescence excitation spectrum with the absorption spectrum of the compound in the vapor phase. The result indicates that the strong decrease in the relative fluorescence yield at higher energies is due mostly to a decrease in the radiative decay rate of the emitting state. Comparison of the experimental results with the TDDFT potential energy curves for excited states strongly suggests that the decrease in the radiative decay rate of the aminobenzonitriles at higher energies is due to the crossing of the pi pi* singlet state by the lower-lying pi sigma*(C[triple bond]N) singlet state of very small radiative decay rate. The threshold energy for the fluorescence "break-off" is in good agreement with the computed energy barrier for the pi pi*/pi sigma* crossing. For NN, on the other hand, the observed decrease is in fluorescence yield at higher excitation energies can best be attributed to the crossing of the pi pi* singlet state by the pi sigma* triplet state.

Computational chemistry can give information about the probable conformations of reactive intermediates that are difficult to determine experimentally. Based on density functional theory (DFT) calculations of tetra-O-methyl-D-mannopyranosyl and -glucopyranosyl oxacarbenium ions, two families of conformations, which we call B0 and B1, were found. For the manno configuration, a 4H3 and 3E almost isoenergetic pair were found, whereas for the gluco-configuration a 4H3 and 5S1 pair favouring 4H3 were calculated. These results corroborate earlier results and suggest that this two or more conformer hypothesis is general. Nucleophilic attack on these pairs of cations was modelled with methanol and led to four cases to consider namely alpha- or beta-attack on B0 or B1. The resulting complexes (G0, G1 and F0, F1) demonstrate facial selectivity. The relative energies of these complexes are dominated by intramolecular hydrogen bonding and the conformational consequences to the pyranose ring of changes in the C-5-O-5-C-1-C-2 torsion angle. Constrained variation of the nucleophilic oxygen (methanol) to C-1 distance shows that these ion dipole complexes are the only minima with this constraint.

Unlike fluorinated benzenes with four or less fluorine atoms, pentafluorobenzene (PFB) and hexafluorobenzene (HFB) exhibit very small fluorescence yields and short fluorescence lifetimes. These emission anomalies suggest that the nature of the first excited singlet (S(1)) state may be different for the two classes of fluorobenzenes. Consistent with this conjecture, the time-dependent density-functional theory calculations yield S(1) state of pi pi(*) character for fluorinated benzenes with four or less F atoms, and S(1) state of pi sigma(*) character for PFB and HFB. The pi sigma(*) character of the S(1) state of PFB and HFB has been confirmed by laser-induced fluorescence, which reveal the presence of a new electronic transition to the red of the (1)pi pi(*) (L(b))<--S(0) transition, which can be identified with the predicted low-energy (1)pi sigma(*)<--S(0) absorption. The low fluorescence yields and the short fluorescence lifetimes of PFB and HFB are consistent with the small radiative decay rate of the (1)pi sigma(*) state and efficient S(1) (pi sigma(*))-->S(0) internal conversion between two electronic states of very different geometries.

Quantitative measurements of second-harmonic generation optical activity (SHG-OA) have been performed for alpha-helical polypeptides poly-(gamma-benzyl-L-glutamate) and poly-(gamma-ethyl-L-glutamate) adsorbed at the airwater interface, with the fundamental frequency variant Planck's over 2piomega = 2.96 eV (lambda = 417 nm). The chiral component of the nonlinear susceptibility chi(XYZ) ((2)) is small for both polymers, being comparable in magnitude with the susceptibility chi(XXZ) ((2)) of the clean airwater interface. The microscopic origin of the nonlinear response has been investigated by using semiempirical ZINDOS calculations in conjunction with standard time-dependent perturbation theory to evaluate the molecular hyperpolarizability tensor of a model alpha-helix composed of glycine residues. Calculated nonlinear susceptibilities (per monomer unit) are in good agreement with experimental measurements for both the chiral and achiral response. The computational results indicate that charge transfer transitions of the alpha-helix have a large influence on the achiral components of the hyperpolarizability tensor, and produce characteristic features in the response under suitable experimental conditions. The dominant origin of SHG-OA for the model alpha-helix is a structural effect due to the tilt of the plane of each amide group of the helix relative to the helical axis. SHG-OA is associated with the orientational distribution of isolated, achiral chromophores, and is present in the absence of electronic coupling between the amide subunits of the polypeptide alpha-helix.

Comparison of the TD-BP86cc-pVDZ electronic excitation energies and the CIScc-pVDZ vibrational frequencies of 4-dimethylaminobenzonitrile with the available experimental data indicates that the picosecond transient absorption at about 700 nm, and the excited-state vibration of frequency 1467 cm(-1), belong to the lowest-energy pisigma(CN) (*) state of bent geometry (CCN bond angle of about 120 degrees and a large CN bond distance). Consistent with these assignments, the 1467 cm(-1) Raman band, attributed to the CN stretch, exhibits a large resonance enhancement of intensity when the probe (Raman excitation) wavelength is set to the spectral region of the pisigma(*)<--pisigma(*) absorption. The result corroborates the occurrence of an ultrafast state switch from the initially excited (1)pipi(*) (L(b)) state to the (1)pisigma(*) state of lower energy.

Evidence is presented which indicates that the photoinduced intramolecular charge transfer (ICT) in 4-dimethylaminobenzonitrile proceeds by a new mechanism in which pi sigma(C triple bond N) (*) state is the intermediate of a consecutive process that takes the initially excited pi pi(*) state to the fully charge-separated ICT state. The absence of the ICT-state formation in 4-aminobenzonitrile is attributed to the smaller electron-donor strength of the amino group relative to the dimethylamino group, which hinders the pi sigma(*)-->ICT charge-shift reaction.

Local density and generalized gradient approximation time-dependent density functional methods have been used for calculation of the singlet and triplet excited states of nickel-porphine, Ni-tetraphenyloporphine, and Ni-octaethyloporphyrine. Special attention is paid to metal-ligand transitions and d-d transitions. It is shown that the lowest exited singlet states of the three compounds can be described as a transfer of an electron from the porphine ring to the d(x2-y2) orbital of the nickel atom. On the other hand, the lowest excited triplet state arises from promotion of an electron between two nickel d orbitals, an occupied d(z2) and an empty d(x2-y2). It is proposed that a rapid quenching of the excited singlet states is due to an ultrafast intersystem crossing between 1Eg)and 3Eg or 3B1g states.

We use quantitative experimental and theoretical approaches to characterize the vibrational dynamics of the Fe atom in porphyrins designed to model heme protein active sites. Nuclear resonance vibrational spectroscopy (NRVS) yields frequencies, amplitudes, and directions for 57Fe vibrations in a series of ferrous nitrosyl porphyrins, which provide a benchmark for evaluation of quantum chemical vibrational calculations. Detailed normal mode predictions result from DFT calculations on ferrous nitrosyl tetraphenylporphyrin Fe(TPP)(NO), its cation [Fe(TPP)(NO)]+, and ferrous nitrosyl porphine Fe(P)(NO). Differing functionals lead to significant variability in the predicted Fe-NO bond length and frequency for Fe(TPP)(NO). Otherwise, quantitative comparison of calculated and measured Fe dynamics on an absolute scale reveals good overall agreement, suggesting that DFT calculations provide a reliable guide to the character of observed Fe vibrational modes. These include a series of modes involving Fe motion in the plane of the porphyrin, which are rarely identified using infrared and Raman spectroscopies. The NO binding geometry breaks the four-fold symmetry of the Fe environment, and the resulting frequency splittings of the in-plane modes predicted for Fe(TPP)(NO) agree with observations. In contrast to expectations of a simple three-body model, mode energy remains localized on the FeNO fragment for only two modes, an N-O stretch and a mode with mixed Fe-NO stretch and FeNO bend character. Bending of the FeNO unit also contributes to several of the in-plane modes, but no primary FeNO bending mode is identified for Fe(TPP)(NO). Vibrations associated with hindered rotation of the NO and heme doming are predicted at low frequencies, where Fe motion perpendicular to the heme is identified experimentally at 73 and 128 cm-1. Identification of the latter two modes is a crucial first step toward quantifying the reactive energetics of Fe porphyrins and heme proteins.

We present femtosecond time-resolved photoelectron spectra of adenine in a molecular beam, recorded at pump wavelengths of 250, 267, and 277 nm. This leads to initial excitation of the bright S2(pipi*). Close to the band origin (277 nm), the lifetime is several picoseconds. Higher vibronic levels (267 and 250 nm excitation) show much shorter lifetimes of t < 50 fs, and we observe strong coupling between S2(pipi*) and S1(npi*). Rapid internal conversion (t < 50 fs) populates the lower lying S1(npi*) state which has a lifetime of 750 fs. At 267 nm, we found evidence for an additional channel which is consistent with the dissociative S3(pisigma*) state, previously proposed as an ultrafast relaxation pathway from S2(pipi*).

Time-resolved photoelectron spectroscopy (TRPES) is emerging as a useful tool for the study of non-adiabatic dynamics in isolated polyatomic molecules and clusters due to its sensitivity to both electronic and vibrational dynamics. A powerful extension of TRPES, coincidence imaging spectroscopy (CIS), based upon femtosecond time-resolved 3D momentum vector imaging of both photoions and photoelectrons in coincidence, is a new technique for the study of complex dissociative processes. Here we show how these spectroscopies can be used to study both non-adiabatic intramolecular and photodissociation dynamics in polyatomic molecules. Intramolecular dynamics in the alpha, beta-enones acrolein, crotonaldehyde and methyl vinyl ketone are studied using both TRPES and laser-induced fluorescence of HCO(X) product yields. The location of the methyl group is seen to have very dramatic effects on the relative electronic relaxation rates and the HCO(X) yield. Applying both TRPES and CIS to the 200 nm and 209 nm photodissociation of the nitric oxide dimer, (NO)2, we observe the fs time-scale evolution of the excited parent neutral via its photoelectron spectrum and the emergence of the NO(A) photofragment including its energy and angular distributions.

A series of iron complexes based on the pentadentate ligand 4,7-bis(2'-methyl-2'-mercaptopropyl)-1-thia-4,7-diazacyclononane), (bmmp-TASN)(2)(-), have been synthesized and characterized as models of iron-containing nitrile hydratase (NHase). The chloro derivative [(bmmp-TASN)Fe(III)Cl].0.5EtOH (1) contains a labile chloride which facilitates synthesis of related complexes via substitution reactions. Complex 1 is high-spin, g = 4.28. Addition of NEt(4)CN with 1 in CH(2)Cl(2) results in the cyanide ligated complex [(bmmp-TASN)Fe(III)CN] x 0.5EtOH (2), which shows a single intense nu(CN) band at 2083 cm(-)(1) in the IR region. Complex 2 is low-spin, g(1) = 2.31, g(2) = 2.16, and g(3) = 1.96. Under basic conditions complex 1 affords a mu-oxo bridged dimeric Fe(III) complex [(bmmp-TASN)Fe(III)](2)O (3), which shows an intense band at 799 cm(-)(1). Complex 3 was recrystallized from CH(2)Cl(2)/hexane solution in the triclinic space group P1, with a = 10.5486(15) A, b = 13.0612(19) A, c = 8.1852(12) A, alpha = 96.923(2) degrees, beta = 112.729(2) degrees, gamma = 81.048(2) degrees, and Z = 1. Density functional theory (DFT) calculations of the previously communicated iron-nitrosyl complex [(bmmp-TASN)Fe(III)(NO)][BPh(4)] (4) (Inorg. Chem. 2002, 41, 1039-1041) reveal that the HOMO region is dominated by Fe-S bonding. Complexes 1-4 display irreversible or quasi-reversible reductions in the cyclic voltammograms. All of the iron complexes and the zinc derivative, (bmmp-TASN)Zn (5), display an irreversible oxidation. Complex 5 was crystallized in the monoclinic space group P2(1)/n with a = 9.5759(6) A, b = 20.9790(13) A, c = 10.7113(7) A, beta = 91.283(1) degrees, and Z = 4.

The excited-state dynamics of trans-azobenzene were investigated by femtosecond time-resolved photoelectron spectroscopy and ab initio molecular dynamics. Two near-degenerate pipi* excited states, S2 and S3,4, were identified in a region hitherto associated with only one excited state. These results help to explain contradictory reports about the photoisomerization mechanism and the wavelength dependence of the quantum yield. A new model for the isomerization mechanism is proposed.

FeNO vibrational frequencies were investigated for a series of myoglobin mutants using isotope-edited resonance Raman spectra of (15/14)NO adducts, which reveal the FeNO and NO stretching modes. The latter give rise to doublet bands, as a result of Fermi resonances with coincident porphyrin vibrations; these doublets were analyzed by curve-fitting to obtain the nuNO frequencies. Variations in nuNO among the mutants correlate with the reported nuCO variations for the CO adducts of the same mutants. The correlation has a slope near unity, indicating equal sensitivity of the NO and CO bonds to polar influences in the heme pocket. A few mutants deviate from the correlation, indicating that distal interactions differ for the NO and CO adducts, probably because of the differing distal residue geometries. In contrast to the strong and consistent nuFeC/nuCO correlation found for the CO adducts, nuFeN correlates only weakly with nuNO, and the slope of the correlation depends on which residue is being mutated. This variability is suggested to arise from steric interactions, which change the FeNO angle and therefore alter the Fe-NO and N-O bond orders. This effect is modeled with Density Functional Theory (DFT) and is rationalized on the basis of a valence isomer bonding model. The FeNO unit, which is naturally bent, is a more sensitive reporter of steric interactions than the FeCO unit, which is naturally linear. An important additional factor is the strength of the bond to the proximal ligand, which modulates the valence isomer equilibrium. The FeNO unit is bent more strongly in MbNO than in protein-free heme-NO complexes because of a combination of a strengthened proximal bond and distal interactions.

Synchrotron far-IR spectroscopy and density-functional calculations are used to characterize the low-frequency dynamics of model heme FeCO compounds. The "doming" vibrational mode in which the iron atom moves out of the porphyrin plane while the periphery of this ring moves in the opposite direction determines the reactivity of oxygen with this type of molecule in biological systems. Calculations of frequencies and absorption intensities and the measured pressure dependence of vibrational modes in the model compounds are used to identify the doming and related normal modes.

An Al-cytosine association complex has been generated via laser ablation of a mixture of aluminum and cytosine powders that were pressed into a rod form. The ionization energy of the complex is found to be 5.16 +/- 0.01 eV. The photoionization efficiency spectrum of Al-cytosine has also been collected. DFT calculations indicate that binding of Al to cytosine manifests a significant weakening of the N-H bond, predicted to have a strength of 1.5 eV in the complex, and a significant stabilization of the oxo tautomeric form relative to the hydroxy forms. The predicted ionization energy of 5.2 eV agrees well with the experimental value. The threshold for dehydrogenation/ionization of Al-cytosine, forming (Al-cytosine-H)+, is found to occur at photoexcitation energies between 11.4 and 12.8 eV. This is a two-photon process that is proposed to occur via photoinduced electron transfer from Al to an antibonding (sigma) orbital localized on N-H. In the context of this mechanism, this work constitutes the first time charge transfer between a metal and DNA base has been photoinitiated in the gas phase.

Femtosecond time-resolved photoelectron spectroscopy is emerging as a new technique for investigating polyatomic excited state dynamics. Due to the sensitivity of photoelectron spectroscopy to both electronic configurations and vibrational dynamics, it is well suited to the study of non-adiabatic processes such as internal conversion, which often occur on sub-picosecond time scales. We discuss the technical requirements for such experiments, including lasers systems, energy- and angle-resolved photoelectron spectrometers and new detectors for coincidence experiments. We present a few examples of these methods applied to problems in diatomic wavepacket dynamics and ultrafast non-adiabatic processes in polyatomic molecules.